Question: extract some feature from peak?
gravatar for star
7 months ago by
star190 wrote:

I did peak calling using MACS2. Now I like to calculate some features (like below) from them but I am not sure which tools can be helpful.

  • peak height
  • number of read / count for each peak -- > I think map / genomecoverage function of bedtools may be helpful but I am not sure!

Thanks for your help in advanced.

ADD COMMENTlink modified 7 months ago • written 7 months ago by star190

you may use some tools in bedtools suite- intersecting the bam with the intervals bed file by intersectBed, use coverage to compute depth and breadth, and even genomecov and an in house script.

ADD REPLYlink written 7 months ago by biobiu110
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